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<h1 class="epydoc">Identifier Index</h1>
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[
 <a href="identifier-index-A.html">A</a>
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 <a href="identifier-index-C.html">C</a>
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  X
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]
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<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="S">S</a></h2></td>
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<table class="link-index" width="100%" border="1">
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<td width="33%" class="link-index"><a href="moltk-module.html#s">s</a><br />
<span class="index-where">(in&nbsp;<a href="moltk-module.html">moltk</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.gui.moltk_ui.Ui_MoltkMainWindow-class.html#setupUi">setupUi()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.gui.moltk_ui.Ui_MoltkMainWindow-class.html">Ui_MoltkMainWindow</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#STAGE_SCORER">STAGE_SCORER</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.gui.structure_renderer.StructureRenderer-class.html#sceneChanged">sceneChanged</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.gui.structure_renderer.StructureRenderer-class.html">StructureRenderer</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk-module.html#sin">sin()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk-module.html">moltk</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html#STAGE_SCORER">STAGE_SCORER</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Stage-class.html">Stage</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.Aligner.TargetPosition-class.html#score">score()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.TargetPosition-class.html">TargetPosition</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Quaternion-class.html#size">size()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Quaternion-class.html">Quaternion</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#STAGE_SEQUENCE">STAGE_SEQUENCE</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.Alignment-class.html#score">score()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Alignment-class.html">Alignment</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.QueryPositionList-class.html#sort">sort()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.QueryPositionList-class.html">QueryPositionList</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html#STAGE_SEQUENCE">STAGE_SEQUENCE</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Stage-class.html">Stage</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.Aligner.Scorer-class.html">Scorer</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.TargetPositionList-class.html#sort">sort()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.TargetPositionList-class.html">TargetPositionList</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#STAGE_TABLE_INITIALIZED">STAGE_TABLE_INITIALIZED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.Alignment.Row-class.html#sequence_weight">sequence_weight</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Alignment.Row-class.html">Row</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.std_vector_int-class.html#sort">sort()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.std_vector_int-class.html">std_vector_int</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html#STAGE_TABLE_INITIALIZED">STAGE_TABLE_INITIALIZED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Stage-class.html">Stage</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.Aligner.Scorer-class.html#set_end_gaps_free">set_end_gaps_free()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Scorer-class.html">Scorer</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html">Stage</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#STAGE_TRACED">STAGE_TRACED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#set_end_gaps_free">set_end_gaps_free()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#STAGE_ALLOCATED">STAGE_ALLOCATED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html#STAGE_TRACED">STAGE_TRACED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Stage-class.html">Stage</a>)</span></td>
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<td width="33%" class="link-index"><a href="moltk.Rotation3D-class.html#set_from_angle_about_unit_vector">set_from_angle_about_unit_vector()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Rotation3D-class.html">Rotation3D</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html#STAGE_ALLOCATED">STAGE_ALLOCATED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Stage-class.html">Stage</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.std_vector_int-class.html">std_vector_int</a><br />
<span class="index-where">(in&nbsp;<a href="moltk-module.html">moltk</a>)</span></td>
</tr>
<tr>
<td width="33%" class="link-index"><a href="moltk.Quaternion-class.html#set_from_angle_axis">set_from_angle_axis()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Quaternion-class.html">Quaternion</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#STAGE_EMPTY">STAGE_EMPTY</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.gui.structure_canvas-module.html">structure_canvas</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.gui-module.html">moltk.gui</a>)</span></td>
</tr>
<tr>
<td width="33%" class="link-index"><a href="moltk.Rotation3D-class.html#set_from_quaternion">set_from_quaternion()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Rotation3D-class.html">Rotation3D</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html#STAGE_EMPTY">STAGE_EMPTY</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Stage-class.html">Stage</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.gui.structure_renderer-module.html">structure_renderer</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.gui-module.html">moltk.gui</a>)</span></td>
</tr>
<tr>
<td width="33%" class="link-index"><a href="moltk.Alignment-class.html#set_score">set_score()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Alignment-class.html">Alignment</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner-class.html#STAGE_RECURRENCE_COMPUTED">STAGE_RECURRENCE_COMPUTED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner-class.html">Aligner</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.gui.structure_canvas.StructureCanvas-class.html">StructureCanvas</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.gui.structure_canvas-module.html">moltk.gui.structure_canvas</a>)</span></td>
</tr>
<tr>
<td width="33%" class="link-index"><a href="moltk.gui.structure_renderer.StructureRenderer-class.html#setupCamera">setupCamera()</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.gui.structure_renderer.StructureRenderer-class.html">StructureRenderer</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.Aligner.Stage-class.html#STAGE_RECURRENCE_COMPUTED">STAGE_RECURRENCE_COMPUTED</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.Aligner.Stage-class.html">Stage</a>)</span></td>
<td width="33%" class="link-index"><a href="moltk.gui.structure_renderer.StructureRenderer-class.html">StructureRenderer</a><br />
<span class="index-where">(in&nbsp;<a href="moltk.gui.structure_renderer-module.html">moltk.gui.structure_renderer</a>)</span></td>
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